comparison qiime/collate_alpha.xml @ 0:003162f90751 draft

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author azuzolo
date Wed, 06 Jun 2012 16:40:30 -0400
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1 <tool id="collate_alpha" name="collate_alpha" version="1.2.0">
2 <description>Collate alpha diversity results</description>
3 <requirements>
4 <requirement type="binary">collate_alpha.py</requirement>
5 </requirements>
6 <command interpreter="python">
7 qiime_wrapper.py
8 --galaxy_outputdir=$output1.extra_files_path
9 --galaxy_new_files_path='$__new_file_path__'
10 --galaxy_logfile=$output1
11 --galaxy_new_datasets='^\S+\.txt$:txt'
12 --galaxy_datasetid=$output1.id
13 collate_alpha.py
14 --input_path=$input_path.extra_files_path
15 --output_path='$__new_file_path__'
16 </command>
17 <inputs>
18 <param name="input_path" type="data" format="txt" label="input_path"
19 help="Input is alpha diversity log file [REQUIRED]"/>
20 <!--<param name="example_path" type="text" label="example_path"
21 help="example alpha_diversity analysis file, containing all samples and all metrics to be included in the collated result[Default: chosen automatically (see usage string)]"/>-->
22 </inputs>
23 <outputs>
24 <data format="txt" name="output1" label="${tool.name} on ${on_string}"/>
25 </outputs>
26 <tests>
27 </tests>
28 <help>This tool concatenates all the files generated by alpha_diversity in order to generate rarefaction curves. The input is therefore the log file generated by alpha_diversity, and the output is a log file listing all the output files, as well as the files themselves. Galaxy must be manually refreshed after running this tool to view all output files.
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30 For more information, see collate_alpha_ in the Qiime documentation.
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32 Updated and validated 01/16/12 by Amanda Zuzolo, Microbiome Analysis Center, George Mason University, Fairfax, VA
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34 Qiime integration courtesy Jim Johnson, Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, MN
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36 .. _collate_alpha: http://qiime.org/scripts/collate_alpha.html</help>
37 </tool>
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